Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014835.1 Corchorus olitorius cultivar O-4 contig14868, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 17233
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32


Found at i:156 original size:32 final size:32

Alignment explanation


    Indices: 115--179  Score: 130
    Period size: 32  Copynumber: 2.0  Consensus size: 32

        105 AATGTATCAA

                                            
        115 CACATTCTCTAGCTAAGATTAAGCTGGATAAT
          1 CACATTCTCTAGCTAAGATTAAGCTGGATAAT

                                            
        147 CACATTCTCTAGCTAAGATTAAGCTGGATAAT
          1 CACATTCTCTAGCTAAGATTAAGCTGGATAAT

             
        179 C
          1 C

        180 GTATGGTGCG


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  32   33  1.00

ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31


Consensus pattern (32 bp):   
CACATTCTCTAGCTAAGATTAAGCTGGATAAT

Found at i:6861 original size:1 final size:1

Alignment explanation


    Indices: 6857--6887  Score: 53
    Period size: 1  Copynumber: 31.0  Consensus size: 1

       6847 TTTTAAAATT

                 *                         
       6857 AAAAATAAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

       6888 CTAGAGTCTT


Statistics
Matches: 28,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   1   28  1.00

ACGTcount: A:0.97, C:0.00, G:0.00, T:0.03


Consensus pattern (1 bp):   
A

Found at i:10614 original size:16 final size:17

Alignment explanation


    Indices: 10593--10639  Score: 51
    Period size: 19  Copynumber: 2.6  Consensus size: 17

      10583 TTTATAATTT

                               
      10593 TTATTAATAATATATATTA
          1 TTATTAATAATATATA--A

                              
      10612 TTATTAA-AATATAATAA
          1 TTATTAATAATAT-ATAA

                       
      10629 TTATATAATAA
          1 TTAT-TAATAA

      10640 ACGAACGTTC


Statistics
Matches: 25,  Mismatches: 0, Indels: 6
        0.81            0.00        0.19

Matches are distributed among these distances:
  17    5  0.20
  18    8  0.32
  19   12  0.48

ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47


Consensus pattern (17 bp):   
TTATTAATAATATATAA

Found at i:10714 original size:35 final size:35

Alignment explanation


    Indices: 10668--10739  Score: 128
    Period size: 35  Copynumber: 2.1  Consensus size: 35

      10658 TATAAACGAG

                                                
      10668 CACTTAAATGAACAATAAACGAG-CATGTTCGTGAA
          1 CACTTAAATGAACAATAAACGAGTC-TGTTCGTGAA

                                               
      10703 CACTTAAATGAACAATAAACGAGTCTGTTCGTGAA
          1 CACTTAAATGAACAATAAACGAGTCTGTTCGTGAA

              
      10738 CA
          1 CA

      10740 TAAACGAACT


Statistics
Matches: 36,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
  35   35  0.97
  36    1  0.03

ACGTcount: A:0.42, C:0.18, G:0.17, T:0.24


Consensus pattern (35 bp):   
CACTTAAATGAACAATAAACGAGTCTGTTCGTGAA

Found at i:14114 original size:22 final size:22

Alignment explanation


    Indices: 14089--14137  Score: 55
    Period size: 22  Copynumber: 2.2  Consensus size: 22

      14079 AAAATTACAT

                     *             
      14089 TTTCTACCTCTT-AAAATCACGA
          1 TTTCTACCTATTCAAAATCA-GA

                 **               
      14111 TTTCTTTCTATTCAAAATCAGA
          1 TTTCTACCTATTCAAAATCAGA

                 
      14133 TTTCT
          1 TTTCT

      14138 GACTTCTCTT


Statistics
Matches: 23,  Mismatches: 3, Indels: 2
        0.82            0.11        0.07

Matches are distributed among these distances:
  22   16  0.70
  23    7  0.30

ACGTcount: A:0.29, C:0.22, G:0.04, T:0.45


Consensus pattern (22 bp):   
TTTCTACCTATTCAAAATCAGA
Done.